The single-celled ciliate, <italic>Oxytricha trifallax</italic>, like all ciliates, has three distinct genomes in separate organelles. <italic>Oxytricha</italic> has a large, gene-rich mitochondrial genome (~70 kb); a large "scrambled", germline genome (~1 Gb) in the micronucleus; and a compact, but highly amplified somatic genome (~50 Mb) in the massively enlarged macronucleus. This thesis describes the assembly and analysis of the non-scrambled, information-dense <italic>Oxytricha</italic> mitochondrial and macronuclear genomes.
The <italic>Oxytricha trifallax</italic> mitochondrial genome is a highly divergent eukaryotic mitochondrial genome and encodes a few split genes. The mitochondrial chromosome is linear and is capped by mitochondria-specific telomeres. An ~5 kb linear mitochondrial plasmid is capped by the same telomeres, suggesting that linear plasmids may be a vehicle for lateral transfer of telomeres. The mitochondrial plasmid shares a 251 bp, 82% identity region with the mitochondrial genome, likely indicating a genome integration event. The proximity of this shared region to terminal segmental duplications suggest that this plasmid may be partly responsible for the expansion of the <italic>Oxytricha</italic> mitochondrial genome.
The <italic>Oxytricha</italic> macronuclear genome has a radical architecture comprised of the shortest known eukaryotic nuclear chromosomes (~3.2 kb) &mdash; "nanochromosomes" &mdash; ranging from 469 bp to 66 kb. Each nanochromosome typically encodes a single gene with a minimal amount of surrounding non-RNA-coding DNA; 3' "untranscribed" regions are especially short, with polyadenylation sites at a median distance of ~25 bp from the telomeres. Macronuclear nucleotide diversity is very high (SNP heterozygosity is 4.0%) indicating one of the largest known eukaryotic effective population sizes for <italic>Oxytricha trifallax</italic>. However, sequence heterozygosity may diminish both during macronuclear development and stochastic, amitotic nanochromosome segregation during vegetative growth. Additional genomic variation is generated when multiple nanochromosomal isoforms are produced by alternative fragmentation of ~10% of the macronuclear genome. There is also modest variation of nanochromosome amplification between nanochromosomes, with higher amplification of alternatively fragmented than non-alternatively fragmented nanochromosomes. In conjunction with the creation of tens of millions of telomeres per cell, we found that <italic>Oxytricha</italic> has also evolved an intriguing repertoire of telomere end-binding protein paralogs.